Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools
Summary: The growing appetite of behavioral neuroscience for automated data production is prompting the need for new computational standards allowing improved interoperability, reproducibility, and shareability. We show here how these issues can be solved by repurposing existing genomic formats whos...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2018-11-01
|
| Series: | iScience |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004218301822 |
| _version_ | 1811297269395226624 |
|---|---|
| author | Jose Espinosa-Carrasco Ionas Erb Toni Hermoso Pulido Julia Ponomarenko Mara Dierssen Cedric Notredame |
| author_facet | Jose Espinosa-Carrasco Ionas Erb Toni Hermoso Pulido Julia Ponomarenko Mara Dierssen Cedric Notredame |
| author_sort | Jose Espinosa-Carrasco |
| collection | DOAJ |
| description | Summary: The growing appetite of behavioral neuroscience for automated data production is prompting the need for new computational standards allowing improved interoperability, reproducibility, and shareability. We show here how these issues can be solved by repurposing existing genomic formats whose structure perfectly supports the handling of time series. This allows existing genomic analysis and visualization tools to be deployed onto behavioral data. As a proof of principle, we implemented the conversion procedure in Pergola, an open source software, and used genomics tools to reproduce results obtained in mouse, fly, and worm. We also show how common genomics techniques such as principal component analysis, hidden Markov modeling, and volcano plots can be deployed on the reformatted behavioral data. These analyses are easy to share because they depend on the scripting of public software. They are also easy to reproduce thanks to their integration within Nextflow, a workflow manager using containerized software. : Biological Sciences; Genetics; Behavioral Neuroscience; Bioinformatics Subject Areas: Biological Sciences, Genetics, Behavioral Neuroscience, Bioinformatics |
| first_indexed | 2024-04-13T06:01:30Z |
| format | Article |
| id | doaj.art-c358764c1d024973aeaad45ebd6009e4 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-13T06:01:30Z |
| publishDate | 2018-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-c358764c1d024973aeaad45ebd6009e42022-12-22T02:59:25ZengElsevieriScience2589-00422018-11-019244257Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis ToolsJose Espinosa-Carrasco0Ionas Erb1Toni Hermoso Pulido2Julia Ponomarenko3Mara Dierssen4Cedric Notredame5Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, SpainCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, SpainCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, SpainCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, SpainCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain; Corresponding authorCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Corresponding authorSummary: The growing appetite of behavioral neuroscience for automated data production is prompting the need for new computational standards allowing improved interoperability, reproducibility, and shareability. We show here how these issues can be solved by repurposing existing genomic formats whose structure perfectly supports the handling of time series. This allows existing genomic analysis and visualization tools to be deployed onto behavioral data. As a proof of principle, we implemented the conversion procedure in Pergola, an open source software, and used genomics tools to reproduce results obtained in mouse, fly, and worm. We also show how common genomics techniques such as principal component analysis, hidden Markov modeling, and volcano plots can be deployed on the reformatted behavioral data. These analyses are easy to share because they depend on the scripting of public software. They are also easy to reproduce thanks to their integration within Nextflow, a workflow manager using containerized software. : Biological Sciences; Genetics; Behavioral Neuroscience; Bioinformatics Subject Areas: Biological Sciences, Genetics, Behavioral Neuroscience, Bioinformaticshttp://www.sciencedirect.com/science/article/pii/S2589004218301822 |
| spellingShingle | Jose Espinosa-Carrasco Ionas Erb Toni Hermoso Pulido Julia Ponomarenko Mara Dierssen Cedric Notredame Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools iScience |
| title | Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools |
| title_full | Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools |
| title_fullStr | Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools |
| title_full_unstemmed | Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools |
| title_short | Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools |
| title_sort | pergola boosting visualization and analysis of longitudinal data by unlocking genomic analysis tools |
| url | http://www.sciencedirect.com/science/article/pii/S2589004218301822 |
| work_keys_str_mv | AT joseespinosacarrasco pergolaboostingvisualizationandanalysisoflongitudinaldatabyunlockinggenomicanalysistools AT ionaserb pergolaboostingvisualizationandanalysisoflongitudinaldatabyunlockinggenomicanalysistools AT tonihermosopulido pergolaboostingvisualizationandanalysisoflongitudinaldatabyunlockinggenomicanalysistools AT juliaponomarenko pergolaboostingvisualizationandanalysisoflongitudinaldatabyunlockinggenomicanalysistools AT maradierssen pergolaboostingvisualizationandanalysisoflongitudinaldatabyunlockinggenomicanalysistools AT cedricnotredame pergolaboostingvisualizationandanalysisoflongitudinaldatabyunlockinggenomicanalysistools |